Originally Posted by joejones

Two comments to add here:

1) There is no penalty for failing to register a bicycle. It helps you to find the bike if it is stolen, but I know people who have left their bicycles unregistered so that cops don't hold them up doing random registration spot checks. (Common method of checking for undocumented foreigners in some locales.)

2) There are a few structural regulations for bikes in Japan. The main one to be aware of is that bikes are required to have both front and rear wheel brakes, so fixed-gear bikes without brakes are not allowed on Japanese roads. There are also regs about length, reflectors, etc. which you might want to check if your bike is in any way non-standard.